################################################### ### chunk number 1: ################################################### #line 93 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" ## load up the library library(RMAGEML) ################################################### ### chunk number 2: ################################################### #line 106 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" ## create marrayRaw object datadir <- system.file("MAGEMLdata", package="RMAGEML") raw <- importMAGEML(directory = datadir, package = "marray", arrayID = "A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median") print(raw) ################################################### ### chunk number 3: ################################################### #line 115 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" ## create marrayRaw object datadir <- system.file("MAGEMLdata", package="RMAGEML") if(interactive()){ raw <- importMAGEML(directory = datadir, package = "marray") } ################################################### ### chunk number 4: ################################################### #line 129 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" #To obtain an marrayInfo object containing the database identifiers of the features present on the array.# data<-system.file("MAGEMLdata", package="RMAGEML") mageom<-importMAGEOM(directory=data) getGnames(mageom, arrayID="A-MEXP-14", DED="DED:707", package = "marray") ################################################### ### chunk number 5: ################################################### #line 141 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" data<-system.file("MAGEMLdata", package="RMAGEML") #To obtain an marrayInfo object containing the database identifiers of the features present on the array.# mageom<-importMAGEOM(directory=data) getArrayLayout(mageom, arrayID="A-MEXP-14", DED="DED:707") ################################################### ### chunk number 6: ################################################### #line 152 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" data<-system.file("MAGEMLdata", package="RMAGEML") #To obtain an marrayInfo object containing the database identifiers of the features present on the array.# mageom<-importMAGEOM(directory=data) gnames<-getGnames(mageom, arrayID="A-MEXP-14", DED = "DED:707", package = "marray") layout<-getArrayLayout(mageom, arrayID="A-MEXP-14", DED = "DED:707") raw <- makeMarrayRaw(mageOM=mageom, layout = layout, gnames = gnames, directory = data, arrayID="A-MEXP-14", DED = "DED:707",QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median") ################################################### ### chunk number 7: ################################################### #line 169 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" ## create RGList object datadir <- system.file("MAGEMLdata", package="RMAGEML") raw <- importMAGEML(directory = datadir, package = "limma", arrayID="A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median") print(raw) ################################################### ### chunk number 8: ################################################### #line 182 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" data<-system.file("MAGEMLdata", package="RMAGEML") #To obtain an marrayInfo object containing the database identifiers of the features present on the array.# mageom<-importMAGEOM(directory=data) genes<-getArrayLayoutLimma(mageom, arrayID = "A-MEXP-14", DED="DED:707") print(genes[1:10,]) ################################################### ### chunk number 9: ################################################### #line 193 "vignettes/RMAGEML/inst/doc/RMAGEML.Rnw" data<-system.file("MAGEMLdata", package="RMAGEML") #To obtain an marrayInfo object containing the database identifiers of the features present on the array.# mageom<-importMAGEOM(directory=data) genes<-getArrayLayoutLimma(mageom, arrayID = "A-MEXP-14", DED = "DED:707") raw<- makeRG(mageOM=mageom, genes = genes, directory=data, arrayID="A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")